Naruto: The One
by BloodRedSword23
Summary: The Matrix Xover, Experimental fan fic, Naruto is walking around Konoha after being neglected for his two sisters, he falls into a cave and discovers the remnants of Machine city, what happens when he meets Neo? Strong Naruto! Parents Alive! NarutoxShizuka Constructive criticism please
1. Chapter 1

**Okay, this is a new story idea that just popped in my head, its an experimental story, basically I am going to publish this chapter, see how it does and decide if i should continue from there.**

**Yes it is similar to other stories, but with a few different twists, like i said, I'm not exactly sure how this story will turn out, if i get a good enough feedback on it, i will continue it...if i don't...Meh i don't know.**

**Anyway, tell me what you guys think, please leave only constructive criticism.**

**Also, I kinda wrote this chapter in like ten minutes, So my grammer probably isn't that good.**

* * *

Naruto's POV

Naruto was watching as his parents were ignoring him in favor of his twin sisters…again. It had been going on like this ever since they had been born. He had been born on the day of the nine tailed fox attack, so it was obvious that he became the jinchurikki for it. It was because of his Father's sensei Jiraiya giving himself up for the sealing. And then two years later his mom had a pair of twin daughters. After that he sort of…faded away,His parents just seemed to favor them more. Not only had that happened, but they even seemed to be training them at a young age. They didn't offer to do that with him, their excuse for not training him was one sentence.

"_You have the nine tailed fox protecting you, so you don't need our techniques as much as your sisters. You'll learn in the academy." _That was the answer that his parents had given him.

Seriously? Just because he was the host for a demon doesn't mean it would help him become a great ninja automatically! That was stupid to believe that. So most of the time he was training by himself…in secret of course, his parents would probably get pissed if they found out he was training by himself when they ordered him not to. As of right now he was working on low level ninjutsu. He started the academy tomorrow, so he wanted to be prepared.

Pretty soon, after tomorrow, he wouldn't have to worry about not being able to train anymore because of his parents not allowing him. As soon as he entered the academy, he would be allowed to train by himself, and nothing would stop him, of course, nothing was stopping him before. He hated the fact that his parents were training his siblings and not him. For example, they were two years younger, wasn't there a rule saying that it was dangerous to train someone at their age. After all, the age he was at right now was considered the standard age for entering the academy, so why did his parents choose to train his siblings? Was there something wrong with him?

He was currently doing Kata from a scroll he got from his godmother and his grandfather. As it turns out his godmother Tsunade acted more like a mother than his actual mother, she was there for him most of the time whenever he had a problem, and even though she didn't exactly like the idea of him becoming a ninja, she supported him. As for his grandfather, he was the third hokage, the one who was in office before his father.

He had first met the old man when Tsunade introduced him when he came for a visit. As it turned out, the old man and Naruto got along fine. In fact they had started to bond after a while. In fact, it seemed that he had close bonds with people who didn't even seem to be related to him at all. The prime examples were his friends Kurenai, Anko, Yugao, Itachi, Genma, Ibiki, Might Guy, and most of the Inuzuka clan. He had met them all when he was wandering around Konoha one day, he noticed that they all seemed to be hanging out at this one restaurant in the leaf. They had invited him over because he was eating alone and looked like he needed some company.

He told them about how his family ignored him; they were all disgusted that the fourth hokage treated his own family this way. You didn't neglect your own son for his two sisters. Itachi's father may have been a prick, but at least he sometimes acted like a better parent than Naruto's. From that day forward, they tried to spend as much time with him as possible. However they were busy most of the time with missions, so Naruto didn't see them too often.

* * *

**TWO DAYS LATER**

Naruto had just gotten out of the academy; he had made friends with his new instructor Iruka. He didn't look at him as the hokage's son, which was a relief because Naruto thought his dad was a prick. Although, there was one thing about Iruka he didn't like, he really loved to hear himself talk in his lectures. And he thought the hokage speeches were long winded, but this guy could put you to sleep by talking!

Either way, he was going to one of the training grounds to see if Anko was around, she and the others promised that they would help with his training. He was taking a shortcut to get to the training ground, as he was thinking about the type of training Anko was going to put him through. He suddenly felt his foot fall through a hole in the ground.

"Dang it!" He yelled as he tried to pull his leg free, from the looks of things it looked as if his leg was caught in a snake hole.

"Perfect, on my way to training, and I get my foot stuck in a hole, way to go Shinobi in training." Naruto said as he kept trying to get his foot out.

All of a sudden he heard cracking and the sound of what dirt falling onto the ground.

"That…can't be good." He said as the ground suddenly gave out underneath him.

"OH NOOOOO!" He yelled out as he suddenly was falling and rolling down a long metallic tube.

He was going deeper and deeper into the ground as he trying to stop himself from falling any further, but the walls around him were too slippery as he continued to fall down. But then, as quickly as it started, he suddenly stopped and fell straight on the ground of a cold metallic floor.

"Ow…that sucked." He said as he got up and looked around.

It was dark in the cave that he had fallen into. There was barely any light, so he reached into his pockets. Luckily he had a small amount of flash paper that was modified to act like a torch. For once he was thanking his father for creating a seal like that. He activated the seal and looked around. As he suspected, the cavern had a metal alloy on the walls, but what was interesting were the designs, there seemed to be some strange markings on the cave as well as hundreds of random wires hanging around, what was this place? An underground power plant or something? Naruto figured, since he obviously couldn't get back up the way he came, he might as well look for another way out,

As he made his way through the city, he couldn't help but be amazed at what he was saying. This cave, it was like it was an underground city! There were even these weird statues of these strange squid like beings on the walls. As he continued his walk through the city/cave, he came across a ledge where he got a good look at the whole city, the place was void of any life. There weren't even any worms, it was just dead, there couldn't be anything worthwhile down here…Or…so Naruto thought.

As soon as he took another step forward, his foot was suddenly caught in the grip of a Metallic claw. The next thing he knew was that he was being leaned backwards, and the wires on the walls were coiling around him. There were soon more strange tendrils with more claws and other devices that started drilling holes into his arms and legs.

"AGGGGGHHH!" Naruto screamed as they drills installed these strange plugs into his arms and legs, and he even felt one drilling in the back of his head.

He was screaming in agony as not only were the plus installed in his body, but soon there were other wires being plugged into the plugs on his arms and legs. Pretty soon, he suddenly felt something stab into his head and everything went black.

* * *

**IN THE MATRIX**

Naruto woke up in a white room as if he was waking from a nightmare, he looked at his arms and legs and saw that the plugs were gone, in fact there was no sign that anything happened to him at all. He sighed in relief as if he believed it was all just a dream.

"Well this is certainly strange." He heard a man's voice say as he turned around.

He saw a man wearing a black trench coat that and black sunglasses. On second thought, the man was wearing black everywhere; it was almost as if the man had no idea there was any other color in the world. His skin was a pale shade and his hair was black and slicked. The man had a blank look on his face as if he didn't care about anything.

"Who are you?" Naruto yelled as the man just held up a hand.

"If you think that I am your enemy, then you are mistaken." He said as Naruto was still looking at the man with distrust.

"You didn't answer my question." He said as the man got a slight smirk.

"My name Is Neo." He said as the room suddenly turned into a living room of some building.

"Please...take a seat." Neo said as Naruto was still shocked that the room turned from a white room to a living room….What the hell kind of dream was this?

"And what is your name?" Neo asked as Naruto sat down in a recliner.

"Naruto Uzumaki." He said as he stared at the man with a confused look.

"Tell me Mr. Uzumaki, do you know where you are?" He asked as Naruto just looked at him with a strange look on his face.

"Isn't this a dream, along with that weird ass city I found?" He asked as Neo shook his head.

"That weird ass city, is the remains of Machine city, and right now…you are in the matrix." He said as Naruto just got even more confused.

"Uhm, what the hell is all this?" He asked as Neo sighed and just put his hand up to Naruto's forehead.

The next thing that Naruto knew was that images were flying through his heads, images of men in suits dodging bullets, images of Neo fighting off these men like they were nothing. Images of a woman and a group of men in trench coats that were fighting. All the information was running through his mind like a speeding bullet.

Soon enough, Naruto collapsed back into his chair and looked at Neo.

"Are you telling me, that humans used to be ruled over by machines, and they used the matrix to keep us enslaved, and you were part of a group that fought against the machines, and you were something known as…The One?" He asked as the download of information had affected him.

"Yes, I trust that the transfer of information has filled you in on these subjects?" He asked as Naruto nodded.

His head hurt like hell from all the Data, but he could understand all of what Neo was trying to say.

"And you fought against a rogue program called Smith, and in the end, he was destroyed…but…in the memory, it would appear that you were killed too….I don't understand." Naruto said as he saw Neo die in the memories.

If that was true, what was he doing here?

"I don't exactly understand myself, If you died in the matrix you died in real life, I don't understand why I am still alive. If I had to guess, my mind was transferred into a computer in Machine city….but enough of that…why don't you tell me about yourself?" Neo asked as Naruto cleared his throat.

Naruto started to explain that he found Machine city buried underground, and it looked like it hadn't been in use for centuries. He also told him that he lived in an era of shinobi and that the technology that Neo had shown him in the matrix didn't exist and seemed too advanced for them to use. Neo was shocked that technology seemed to have devolved from when he fought the machines. Naruto had also told Neo of his personal life, and how his parents favored his sisters over him. That made Neo show some emotion in the form of anger, that a parent could do that to a child.

"I must say, that is a lot to take in….tell me Naruto, do you want to get stronger?" Neo asked as Naruto nodded.

"Then why don't I train you?" Neo asked as Naruto looked confused.

"How could you do that? You're in this…matrix, and I live in the real world." Naruto said as Neo stood up.

"True, but the matrix could actually help you; didn't you learn anything from my memories?" Neo said as Naruto remembered that Neo had trained in the matrix.

"Oh yeah, but, what about some of the other abilities you displayed…could I…do that?" Naruto asked as Neo thought about it.

"Yes….I was able to use some of my abilities outside of the matrix, I believe you could too, due to this…Chakra you have, and your abilities might even be enhanced." Neo said as Naruto smiled.

"Will you train me?" Naruto asked as Neo nodded.

"Yes, even if the war with the machines is over….I believe that this world of yours needs a new savior." Neo said as he looked at Naruto.

"I will begin a download of information into your brain, I warn you, it can be a little…unpleasant." Neo said as Naruto suddenly had another surge of information going into his brain.

* * *

**In the real world**

You could see Naruto stuggling in the wires that held him in place. Slowly but surely, the wires were starting to unplug themselves, and he was starting to wake up from his trance. Naruto was breathing heavily as the last wire in his head unplugged itself and his eyes opened.

"I know Kung fu." He said as he blinked.


	2. Training And Friendship

**Okay, it would appear that the viewers have decided, i will continue this fan fic since it seems to be doing good so far, and not to mention, since i watched the matrix series again, i guess i do have some motivation for writing this story. So its official, the story will go on.**

**Now, in answer to some of your reviews, if Minato and Kushina do anything to try and make it up to Naruto...well...Meh, I'm trying to think of what to do for that. So with any luck you will get what you want.**

**Anyway, so far so good, The pairing is still NarutoxShizuka mostly due to the fact that I almost never seen anyone use this pairing, so i figured that i might as well give it a try.**

**Plus Since Naruto is pretty much gonna be like Neo, Shizuka is one of the few characters who i could see being like Trinity.**

**But don't worry, Naruto will not suddenly gain Neo's personality, although he will be calm and calculating, he will have SOME of Neo's personality traits..but not all of them.**

**Anyway, i updated this fast because i was in a good mood and i felt like giving you guys another chapter for your reviews...so Enjoy the new chapter of Naruto: The One**

* * *

**Naruto's POV**

Naruto couldn't believe it, he could use a fighting style that he had never heard of until now! But how? Was this some other quirk of the Matrix? If it was, then he definitely liked it. All of a sudden he was cut off when he saw something behind him.

"_I guess you noticed?" _Neo said as he was suddenly on a flat screen.

"Yeah! What did you do?" Naruto said as he was doing some acrobatics and punches.

"_Simple, when I first needed to learn how to fight, Morpheus and the others uploaded the knowledge into my brain, and I picked it up almost immediately...what's really strange Is that you said the exact same thing that I said when I first went through it." _Neo said as Naruto looked at his arms, legs and he felt the back of his head.

"Uhm, Neo….how am I going to hide these plugs?" Naruto asked as Neo looked down.

"_Surely you have clothing with long sleeves on it? And if not you can always cast one of your illusions to prevent anyone from seeing them when you are in public." _Neo said as Naruto nodded at the logic in his words.

He looked around and he noticed that everything in machine city was starting to work and boot up again. Naruto was confused until he looked at Neo.

"_Relax, I control the machines now, they recognize me and you as the masters, so they won't try and start another war with humans." _Neo said as Naruto breathed a sigh of relief.

"So can we upload more information into my brain?" Naruto said as Neo's face nodded.

"_Yes we can, but we can only do one fighting style per day until this whole city is up and running, the place has been shut down for centuries, it takes it a while to boot up." _Neo said as Naruto nodded.

"_Also, the machines have some clothes for you, they are a little torn, but they should do until you can get something better." _Neo said as Naruto turned to see a squid like robot holding a long sleeved black jacket for him, as well as blue jeans.

"Thanks….Squid bot." Naruto said as the machine flew off.

"_I also have another one that should take you to the surface until you learn to fly." _Neo said as Naruto stepped onto the machine.

"Wait a sec, when I learn to FLLLLLLLLLYYYYY!" Naruto screamed as the machine took off.

"_He certainly is an interesting child, that is for sure." _Neo thought as he got to work on machine city, this place may have been his most hated enemy when he was alive, but now he runned everything….if only….Trinity could be with him.

* * *

**WITH NARUTO**

"Woah, that was awesome!" Naruto said as he got off the squid bot and it went back down into the hole.

Luckily the entrance to machine city was already well hidden, so he didn't have to worry about someone else falling in. He made sure that the plugs in his legs, arms and head were covered before he took off running to the training ground to meet Anko.

"Hey Brat! What took you so long?" Anko said as she jumped out from behind and landed on Naruto.

"_Ow! Right on my brand new plug implant!" _He thought as she had landed on the plugs in his spine.

"Sorry, took a wrong short cut." Naruto said as jumped away.

"Anyway, its time for a sparring session, try and hit me if you can." Anko said as Naruto had a flashback from Neo's memories.

"_This is a sparring program similar to the matrix…try and hit me if you can." _Morpheus said in his mind as Naruto copied Neo's opening stance.

Anko raised an eyebrow at the strange fighting style; she had never seen one like the one that Naruto was using. Suddenly he burst forth with speed that he didn't have the day before, weird, it appeared as if his speed had gone up just a little bit in just one day. What the hell happened? Did Guy put weights on his legs?

Suddenly he was punching and kicking her with lightning fast strikes, whenever she blocked one, he just shrugged that off and somehow repositioned his body to get another strike in.

"_What the hell is he doing? Yesterday his Taijutsu was average for an academy student, but now hes at the level of a Genin!" _She thought as she grabbed his foot and spun him around on the ground.

"Good, I got to admit, I wasn't expecting you to be so….fierce." She said as Naruto grinned.

"What can I say….I'm unpredictable." He said as Anko nodded.

"That you are….what was that Style…I've never seen it before." Anko said as Naruto suddenly panicked in his mind.

"_Crap, I can't tell her that the savior of the human race downloaded it into my brain through the matrix…make up a lie!" _Naruto thought as he smiled at her.

"It's a new style I just perfected…I call it…Kung Fu." Naruto said as Anko raised her other eyebrow.

"What a strange name….but a very effective fighting style…it seemed like you always had another strike waiting for me." She said as he smiled at her praise.

"_Even though I didn't really work on it…it was as simple as one two three when it came to learning the style…but at least I can still train in it to make myself better." _Naruto thought as Itachi appeared out of the trees.

"Evening Anko…Naruto." Itachi said with a smile.

Itachi had always liked these two, especially Anko, mostly due to the fact that they were some of the few people around the village who treated him like a human being, and not the invincible anbu captain. Plus even though he would never admit it, he kinda had a thing for Anko. Of course, she already knew that, she was just waiting for him to ask her out. Hell, she practically tried to tease him into saying it, but Itachi, even though he looked like an emotionless shinobi, was actually kind of shy when it came to speaking with women.

"Itachi! You arrived just in time, me and Naruto were having a little spar." Anko said as Itachi nodded.

"I know, I was watching you two, and I have to admit, I was impressed Naruto." Itachi said as Naruto bowed to him.

"Thanks, my style still needs work though." He said as Itachi nodded.

"Its okay, WE WILL ALL help you with that." Itachi said as all of Naruto's friends suddenly came out of the trees.

"Oh man, this is going to hurt." Naruto thought as he got into another stance.

One reason this was going to hurt, was because Guy always freaked out whenever he say a new style of taijutsu being used…so chances are that he was going to be trained into the ground today.

**THREE HOURS LATER**

* * *

"Okay guys, I think Naruto has had enough for today." Kurenai said as they all nodded and Naruto was currently lying down on the ground.

Luckily he only had a few bruises, the only reason that he was laying on the ground was because he was exhausted! Sure fighting one person was hard, but try fighting a whole group of people, it was impossible. The most he could do during the whole match was dodge the blows that were coming at him.

"Thanks Kurenai! I owe you one." Naruto said as he continued to lay on the ground.

It was at that moment that he let his sleeve pull up for a second, and everyone in the group saw a strange metallic object on his arm.

"_What the hell is that?" _Hana and Tsume Inuzuka thought as they noticed that Naruto seemed to have a more…metallic smell to him now.

They all thought that they were just imagining things, so they didn't bother him about it. As soon as he got up he looked up.

"So anyone want to go for some barbecue…I'll pay." Naruto said as all of their eyes widened.

"Naruto, I'm sure you can't pay for all of us." Yugao said as Naruto grinned and held up a fox wallet.

And to say it was stuffed was an understatement.

"Geez! Where did you get all of that?" Anko said as she didn't make that much money in a week!

"I do a bunch of chores around the village, most of the villagers don't mind me helping out, of course some want to give me money just because I'm the hokages son…but I still do work for them, even if it is a gift." Naruto said as he refused to just take money from people without working for it.

"Well, in that case, Lets go get some food…hey Naruto….is it okay with you if I bring Kiba along?" Tsume and Hana asked as Naruto smiled at them.

"Of course, its been a while since I talked to Kibble, for some reason we didn't talk in the academy because we were too busy sleeping." Naruto said as everyone's eyes widened.

"_He was sleeping in the academy and he can fight like that?" _They thought as they all started to walk away.

"Naruto, won't your parents notice your not home for dinner?" Ibiki asked as Naruto stopped and narrowed his eyes.

"I'll be surprised if they notice that I wasn't there yesterday either, I was sleeping outside last night." Naruto said as all of their eyes narrowed at that.

"_What kinds of parents don't notice that their child isn't in the house?" _They all thought as they walked off with Naruto.

* * *

**WITH MINATO AND KUSHINA**

"Ah-Choo!" Both of the parents sneezed as they watched their daughters play with each other.

"What was that about?" Kushina asked as Minato smiled.

"Probably just someone talking about the tale about how we fought the Nine Tailed fox." Minato said as Kushina nodded.

"Most likely, its still told around Konoha all the time." Kushina said as everyone knew the story.

* * *

**WITH NARUTO AND THE OTHERS AT THE RESTAURANT**

Naruto and his friends were all having a good time, Naruto and Kiba had gotten into a rib eating contest, while Kurenai and the others were talking about their training sessions. What nobody could figure out was how fast Naruto was developing, it's almost as if he knew the shadow clone jutsu and was using that training technique to improve his skills faster. But even though Naruto had a lot of chakra, he didn't have enough for the shadow clone yet. Either way, it was really confusing how he had sky rocketed from his performance yesterday to today.

"Hey Naruto, what do you think of Iruka sensei?" Kiba asked as they were chowing down on beef ribs.

"Well, he's a nice guy, but he really needs to tone down his lectures…case in point, how you, I and Shikamaru fell asleep in class." Naruto said as Kiba nodded at that.

"Yeah, sometimes I wish I could record his voice and use it to help me sleep at night, sometimes I sleep better in class than I do on my bed." Kiba said as Hana looked at him.

"That's because you keep falling asleep in the kennels Kibble." Hana said as Kiba blushed in embarrassment.

"Dang it Naruto, now look at what you've started, you say one thing and everyone picks up on it…right?" Kiba said as everyone at the table answered him.

"Not at all Kibble." Everyone said as he just growled at everyone.

"Well, crap." He said as everyone continued to eat.

"Hey come on, Kiba, its not the worst nickname you could have, it's a lot better than dog breath." He said as Kiba looked up.

"For the record, I believe the saying is that a dog's mouth is cleaner than humans." Kiba said as Naruto chuckled.

"True, but you make it sound as if you want that nickname." Naruto said as Kiba shook his head.

"No, I'm just trying to make a point." Kiba said as Naruto stood up and threw a wad of cash on the table.

"Anyway, I should get going…this should be enough for the bill and a tip." Naruto said as Kurenai stopped him.

"Aren't you going to stay a little bit longer?" She asked as Naruto shook his head.

"No, as much as I may dislike it at home, its still better than sleeping outside all the time." Naruto said as he took off.

"Man, Minato and Kushina don't deserve that kid….the happiest kid around, but they don't even acknowledge him." Tsume said as Kiba looked up.

"Maybe they'll sell him to us…how much we got?" Kiba said innocently as everyone sweat dropped.

"No Kiba…We couldn't do that…Right now….we can't do a thing." Hana said even though they wished that Naruto could stay with them.

* * *

**AT THE NAMIKAZE COMPOUND**

Naruto walked in through the door to his home, as soon as he walked in, he felt a huge load of something get put in his arms.

"Good your back, I need you to take the trash out." Kushina said as she didn't even welcome him home.

"Sure." He said as he walked out the door and took out the trash.

He walked back in the house as he saw his so called parents playing with his sister Mito, and sitting on the couch drawing in her sketch pad was his other sister Miu. She was drawing pictures while Mito was playing with their parents. Miu looked at Naruto and gave him a small smile and waved. Naruto waved back, even though he wasn't really close to his family, he did sometimes hang out with Miu and Mito, although they were still too young to realize that he was being neglected because of them.

Either way, he was glad that his sisters were not some pampered princesses, than he would really have a big pain in his ass.

"Hey, I'm going to get some rest, see ya tomorrow." He said as nobody really answered back.

"Yeah sure whatever." Kushina said as he felt a knife get stabbed into his heart.

His own mother just waved him off as if he was a common house pet. Why? Why did she continue to ignore him? He walked upstairs as he ripped off his shirt and looked in the mirror at the plus in his arms and spine.

"You know, it may have hurt to get these things, but I will admit, they kind of look bad ass….and scary." He said as got in bed.

"Well, My parents may not pay attention to me…but…at least…I have my friends…and Neo Sensei." He said as he drifted off to sleep.

Little did he know was that there was a squid bot assigned to watch him in case of any attacks. It would appear that Neo was being more concerned about his safety than his own parents.


	3. Sparring And Tsunade Finds out

**Okay i was feeling a little hyper when i wrote this chapter, so Im not sure how it turned out, mostly because i was just typing as fast as i could. Anyway, this chapter might seem a little rushed, but well, any chapter is better than no chapter, **

**Also for those of you who are asking why he is able to use the powers of the matrix outside of the matrix, well one reason is because like they said in the matrix revolutions the power of the one can sometimes stretch out beyond the matrix and into our world.**

**So basically its like that, But with Naruto its been modified enough to give him any and all abilities...thats all Im gonna say.**

**As for why Kushina and Minato are so neglectful, well, i got a couple of explanations written out, Ill just have to decide which ones to use.**

**Anyone, for everyone who is confused as to why the story is the way it is, you will see. I still got a lot of work to do on this**

* * *

**Naruto's POV**

I had woken up from my dreams, or what could have been a dream. It was mostly a dream that consisted of watching Neo's memories over and over again. I had to admit, he really did live an interesting life. He was able to stop bullets just by thinking it, I mean, that was crazy. Not only that, but some of the knowledge of the technology they used was currently being uploaded into my brain slowly. I got up and cracked my bones, one thing that did not feel good was the fact that the first day I got the plugs embedded in my body, the day after, I was incredibly sore. I guess there was a down side to this after all. But of course, you know what that old saying is, no pain, no gain.

I walked downstairs as I noticed that My mother and father had once again started having breakfast with my siblings, without me. Really? Was It really that much of a chore to wait for me?

"Good, your awake, we got a lot of stuff for you to do when you get home from the academy." Minato said not even looking up from his newspaper.

"Yes Father." I said as Kushina handed me a list of chores and tasks for me to do.

I sat down and while they had a nice breakfast consisting of bacon, eggs, and toast. I had to settle with a bowl of cereal and maybe half a glass of milk. It wasn't the most filling meal, but it did the job. I noticed how my parents, didn't even bother to look at me, I don't understand, they told me that the fox was sealed inside me, and that I wasn't the fox itself, so why did they act so distant? It all started when my two sisters were born. But, I really can't remember that far back; I was like what four years old when they were born? It was hard for me to remember.

Either way, it's like they forgot about me being their son. No, they couldn't have possibly forgotten that fact…could they?

"I better get going." I said as I got my shuriken and kunai holsters.

"Sure, make sure you get all your work done when you get home." Kushina said as she put a piece of bacon in her mouth as I walked out the door.

"It Wouldn't kill you to give me a break." I mumbled under my breath as I walked towards the academy.

* * *

**AT THE ACADEMY**

Naruto had to be careful to hide the metal plugs in his arms and legs, so he was wearing a tight black long sleeved shirt under a dark blue jacket. As well as wearing long black pants on his legs. He didn't have to worry about the one on his head due to the fact that his blond hair covered it. He was cut off from his thoughts as Iruka started his announcements.

"Okay everyone, today we are going to have sparring sessions." Iruka said as Naruto grinned.

"_Thank god, it's a good thing I improved from yesterday…thank you neo sensei." _Naruto thought as everyone stood up and went outside.

"First match, Ino Yamanaka vs Sakura Haruno." Iruka said as Naruto just rolled his eyes.

"_Really? You pit the two biggest Sasuke fan girls in the class to fight against each other? Oh well, at least this will be a good laugh." _He said as Ino and Sakura charged at each other.

Ino came out with a right hook and broke Sakura's nose. Sakura staggered back for a bit but Tackled Ino on the ground and started to rain bombs on her. But when she got a few punches in, Ino caught her last punch and elbowed her in the throat. Even though they had no fighting style, Naruto had to admit…this was getting violent.

"_Okay, Holy Shit….its official, these fan girls are crazy, I thought this was going to be a regular cat fight, but this is pretty brutal." _Naruto thought as both Ino and Sakura passed out.

"Okay, that match ended with a draw." Iruka said as he was a little freaked out by Ino and Sakura.

"Next Match, Naruto Uzumaki Namikaze vs Shikamaru Nara." Iruka said as Shikamaru raised his hand.

"I forfeit, don't want to do this." Shikamaru said as Naruto sweat dropped.

"_Dang it Shika….come on….have some fighting spirit." _Naruto thought as they got to the next match.

It was Kiba vs Shino, due to the fact that it was strictly taijutsu, Kiba won that battle since his family trained in hand to hand more often than the bug clan. After that it was Sasuke vs Ami, she forfeited hoping it would get her on Sasuke's good side….it didn't. Pretty soon, it was Kiba vs Sasuke, and Kiba lost when Sasuke managed to land a good knockout punch.

"Okay, Naruto vs Sasuke." Iruka said as Naruto looked at Sasuke

"_Don't get cocky Naruto, just because you know a new fighting style that is very effective, doesn't mean you shouldn't be cautious." _Naruto thought as they both got into a stance.

Pretty soon, they were charging at each other, Naruto jumped into the air and did a couple of kicks which were blocked by Sasuke. Sasuke counted by doing a high kick, but Naruto leaned back and dodged it. He then grabbed his lag and landed a punch to Sasuke's ribs. Sasuke then kicked his other leg upwards which Naruto again dodged and than landed another spinning back kick to his ribs.

"_Weird, I wasn't this good yesterday." _Naruto said as it almost seemed like Sasuke's kicks were…slower.

"Theres an opening!" Naruto said as he landed a solid punch to Sasuke's midsection which caused him to get the wind knocked out of him.

"Winner Naruto." Iruka said as Naruto started to walk away from the fight.

However Sasuke jumped back up in the air and was going to land a solid punch to the back of Naruto's skull

CRACK!

It seems like that wasn't a good idea.

"OW! SON OF A BITCH! WHAT IS YOUR SKULL MADE OF?" Sasuke said as he now had two broken fingers.

"_Okay Ow, he hit the plug on the back of my head…although two of his fingers are broken, so it was worth it." _Naruto thought as he grinned like a Cheshire cat.

"Okay, I'm going to take Sasuke to get his fingers in a cast, the rest of you work on your taijutsu." Iruka said as he left to get Sasuke bandaged up.

"Woah! Naruto how did you do that, not only did you beat Sasuke, but your hard head broke two of his fingers." Kiba said as he pat Naruto on the back.

"What do you got a metal plate in your head?" Shikamaru asked as Naruto scratched he back of his head.

"_Heh, not exactly….something similar to it though." _He thought as he saw that some of Sasuke's fan girls were still in shock by what they had seen.

* * *

**AT THE END OF THE DAY**

Naruto had finished the academy at least two hours ago, but he was coming back from another training session with Neo in the matrix, apparently they had downloaded a new fighting style called Krav Maga. It was a martial art that was used by Isareli commandos back in Neo's time. Naruto had to admit, learning about the old world was fascinating.

After his sparring session, Neo was trying to make him faster and more acrobatic, obviously since he was able to dodge and stop bullets, and not to mention Trinity could jump across roof tops, it seemed like a good idea. Plus since he was a ninja, those skills would come in handy sometime.

Naruto on the other hand knew that he had to get home and get his work done otherwise his parents would complain about how he didn't do his chores. Funny, the only time they did notice him was when he did something wrong. As he was walking home, he noticed that there were even more squid bots following him.

"_These should be able to get your chores done for you while you continue to train, although I have to admit, using war machines for common household chores is a little….strange." _Neo's voice came from one of the machines as Naruto grinned.

"Thanks Neo Sensei, but won't they notice your machines floating around?" Naruto said as they suddenly turned invisible.

"_I installed them with a cloaking device, you should be fine." _Neo said as Naruto began his walk home.

But the whole time, he was actually training himself, he was jumping from tree to tree hoping to increase his leg strength, not only that, but it would appear that he was picking things up from the matrix a lot faster than anyone else. It was almost like his mind was made for it.

As soon as he got home, he gave the lists of tasks to the squid bots and they quickly disappeared from his sight. But then of course, they were invisible to begin with, it wasn't that hard to get out of his sight. As he walked in, he noticed how nobody was home, he found a note on the table.

"_The family is going out for dinner." _Was written in his parents handwriting.

He frowned a bit at that statement, they forgot about him again.

"Hey kid, why the long face?" He heard a familiar voice say as he turned and saw Tsunade.

"Grandma!" He said as he gave her a love tackle.

"How many times do I have to tell you not to call me that?" She asked as Naruto just grinned up at her.

"How many times do I have to call you that before you realize I'm not going to stop?" Naruto said as Tsunade chuckled.

"Touche." She said as they both sat down on the couch.

"So I heard you beat the top ranking kid in your class….impressive…for a kid." She said as Naruto nodded.

"Yeah for some reason, it just seemed like….I was faster for some reason." She said as Tsunade messed up his hair.

"And apparently you have a hard head too." She said as she suddenly felt something in his head.

"Huh? Whats this?" She said as she parted his hair to look at his head.

"Oh! Its nothing! Nothing at all!" Naruto panicked and Tsunade could tell that something was off.

"Naruto relax, come back here." She said as she grabbed onto his sleeve trying to pull him back.

Why was he freaking out so much? She just felt something weird.

"Its nothing! Just a-"He was cut off as his sleeve was ripped off of his jacket.

He fell to the floor as Tsunade gasped at the sight that she saw. There was Naruto, the child who she thought of as a son, and he had these metal plugs embedded in his arms.

"Naruto! What happened to you?" Tsunade asked as Naruto tried to cover up his arm.

"Its nothing!" He said as Tsunade got a little upset.

"Nothing? Nothing! You have metal parts in your arm? You expect me to believe that's nothing?" She said as Naruto got a little scared.

"Please…its no" He was cut off as a squid bot flew over his head and pinned Tsunade to the wall.

"Ugh…hug." Tsunade said as she was pinned by the mechanical monster in front of her.

"LET HER GO!" Naruto ordered it and it let her fall to the ground.

"Get back to work." He ordered the machine as Tsunade stared at the machine in fright.

"W-what is that thing?" Tsunade asked as Naruto sighed.

"He's….my bodyguard…sorry I guess he saw you as a threat." Naruto said as Tsunade just got even more confused.

"Bodygaurd? But what is that thing? Its definitely not a summon creature!" She yelled as Naruto sighed.

"Well, I guess there is no point in hiding anything now." He said as he started to take off his shirt.

"What are you?" She gasped again as she saw that Naruto had the metal plugs inserted on his spine, his other arm, and he pulled his hair back to show the one in his head.

"What have you done to yourself?" She said as she traced the metal pieces on his back.

"Trust me, this isn't as bad as it looked, its actually….helped me out." Naruto said as Tsunade turned him around.

"How does…THIS help you out?" She said as Naruto sighed.

"I can't tell you…what this is…you have to see it for yourself….follow me." He said as she just got confused and decided that she wanted an explanation…so she followed him.

* * *

**ONE HOUR LATER**

Naruto and Tsunade came out the entrance to Machine City. Tsunade could not believe anything of what she just saw.

"So….your telling me that, you connect to this thing called the Matrix, and this man Neo…was apparently the savior of the human race….and now he is training you…which is why you have improved in the last day?" Tsunade said still a little shocked.

"Yep, that's why I have these plugs in my body." Naruto sighed as Tsunade rubbed her forehead.

"I'll have to tell your parents." She said but Naruto panicked.

"You can't! They will try and destroy the matrix, this is one of the few good things that has happened to me! Please you can't tell them." He said as Tsunade sighed.

"Okay fine…I won't tell them….but….I want to do research on this…Matrix as you call it." Tsunade said as Naruto nodded.

"Of course, it's a done deal." He said as Tsunade smiled a bit.

"In the mean time, I think I need a drink." Tsunade said as Naruto chuckled.


	4. Genin Exams And New Abilities

**Okay I know that this chapter seems a little rushed, the truth was I wasn't sure what to do with the story next, and this chapter does explain what happened to Kushina and Minato, but some of the details will wait until later chapters. So basically i answered your questions, but i also gave you many more to ask.**

**Either way, You all know the drill, enjoy the chapter.**

* * *

**Naruto's POV**

It had been years since Naruto had first discovered the Matrix. They had discovered due to the chakra in his body and the nine tailed fox wanting its host to be strong, that it helped him bring some of the abilities from the Matrix out. And he could use them as if he was jacked in. It was amazing the stuff he was able to do, he pretty much broke all his limits and was now way ahead of anyone in his graduating class. Of course, he had not shown off the matrix abilities in his class other than his taijutsu skills. He figured he didn't want to reveal too much until the time was right.

As a result, he knew almost everyone of the old world martial arts, Neo did not spare him in their training sessions.

He had changed personality wise because of the Matrix, in a way it was like Neo rubbed off on him in some ways. He now had a calm and at times cold demeanor about him. He was only truly happy around those that he cared about, but it would appear that the Matrix did affect him in one way that could be considered negative. It caused him to mature faster than anyone his age. In other words, mentally he felt that he was older than everyone else in his graduating class. But that didn't mean that he was physically underdeveloped. No, ever since he started to train, he only ate stuff that would help keep him healthy and fit for his duty as a ninja.

He had started training with Tsunade and the others more often during those years. He figured he needed to be prepared for any situation, so he tried to train in every possible area of shinobi arts. He had even started to learn different forms of Kenjutsu. Of course, he also learned multiple sword styles from the matrix before training with Yugao. So that allowed him to have a few decent styles in his arsenal.

Over the years, he noticed something….strange. Whenever his parents ignored him, they always seemed to give him the same response whenever he arrived home. The exact same response. It was almost as if they were programmed to act like that. But he just ignored it since he thought that he was just spending too much time in the Matrix. He didn't really have enough time to hang out with his two siblings, he tried to whenever he could, but his training caused him to be busy almost all the time. When he did hang out with them, since they started the academy after he was two years in, he helped them train. But he didn't tell them about the Matrix, that secret was still between him and Tsunade and just recently, the third hokage, he had found out once he noticed that Tsunade and Naruto seemed to disappear a lot, so he followed them one day and discovered the matrix. They made the same deal with him as Naruto made with Tsunade, and as it turned out, the machines actually helped with some of his health problems, so his body felt like it had become younger.

In the mean time, Naruto woke up and looked at his window. The sun was shining brightly in the sky as it was the day of his Genin exam.

"So today is where they test me….very well." He said as a small metal suitcase appeared from under the bed.

He had actually installed a few machines in his home to help him with cleaning and organizing his stuff. So it helped him keep track of everything he owned. As he took the suitcase and laid it on his desk, he looked up and smiled.

"Today is the day I show them what I can really do." He said as he opened up the suitcase.

Inside the case was a completely black outfit. He put on a black t long sleeved shirt as well as Black Combat pants. He put on a pair of black combat boots and over the top of it he put on a black trench coat.

"Oh, I almost forgot." He said as he reached into the case and put on a pair of sunglasses.

All in all, he looked like a miniature version of Neo with Blond hair and whisker marks.

(His outfit is Neo's outfit from Matrix Revolutions)

He also had one thing left, even though it was hard to recreate guns in this world. He had managed to do it, however at the time he didn't have enough material to make more than one handgun. So he picked up the M1911, and he put it in a hidden holster in his trench coat.

He walked downstairs determined to get the academy early, but he was stopped by two girls.

"Hey Big Brother." They said as they looked at his new outfit.

"Hey little sisters." He said as he smiled at them.

He had a bond with them, even though he barely got to see them.

"Nice outfit! Are you gonna graduate today?" Miu said as he nodded.

"Of course…you know me." He said as he walked out the door.

But when Miu and Mito went to follow him, he was already gone.

"Huh, where did he go?" Mito asked as she looked around for her brother.

Little did they know, he had actually flew off as soon as he walked out the door.

* * *

**Minato's POV**

Minato was with Kushina in his office, for some reason he had been feeling strange lately. Kushina had the same feeling as him, but it wasn't a sickness. It was more among the lines of emotional distress. But as of now, they were both sorting some stuff in his office when they came across an interesting flyer.

"Kushina, did you know they are having a tournament to show who is the best trained Genin this year at the academy?" Minato asked as Kushina shook her head.

"No, but who is on the roster." She asked as she sorted some files.

"Let's see, Sasuke Uchiha, Shikamaru Nara, Ino Yamanaka, Sakura Haruno, Choji Akamachi, Hinata Hyuuga, Kiba Inuzuka…" He continued down the list of candidates until one caught his eye.

"Naruto?" He said as Kushina suddenly shot over.

"Naruto? Our son? But….he can't be in the academy yet…can he?" Kushina said as she felt this burning feeling at the back of her head.

"No, I don't remember signing him up for it." Minato said as he felt the same burning feeling as she did.

"Kushina, do you feel a burning feeling?" Minato asked as the pain started to get worse.

"Yeah..it." It suddenly got worse as they both feel to the ground holding their heads.

At that moment, Tsunade and Sarutobi were coming into the office to see if Minato and Kushina would bother to go see their son at the academy tournament. But when they walked in, they noticed how both Minato and Kushina were on the ground groaning in pain and holding their heads.

"Minato! Kushina! Are you alright?" Tsunade said, she might not have agreed with their parenting choices, but she still cared about the two people.

"It burns…it burns." They said as if they were demons covered in holy water.

"What burns..what-" Hiruzen stopped himself as he noticed there was a small seal on Minato's neck.

"_A seal? What the hell is this supposed to be?" _Luckily Hiruzen knew how to get rid of seals so he did a couple of handsigns and placed his hand against the seal.

The seal broke as Minato started to breath heavily. Hiruzen then walked over to Kushina and did the same to her. As they were both breathing heavily, they suddenly looked up at the pair of people.

"Hiruzen, where is Naruto?" Minato said as Tsunade raised an eyebrow.

"Why the sudden concern all of a sudden? After all these years you suddenly want to see him?" Tsunade said as Kushina's head shot up in surprise.

"What do you mean after all these years? It hasn't been that long…has it?" Kushina said as Tsunade got a confused look on her face.

"Kushina, you realize you guys have been neglecting him ever since the twins were born right?" She said as to her shock, Kushina shook her head.

"Tsunade, can I have a word with you?" Hiruzen said as they stepped outside.

"Tsunade, I think that seal that was placed on them, was meant to restrain their memories of Naruto…or something like that, I am not an expert on seals." Hiruzen said as Tsunade looked confused.

"But who would want to place a seal like that on them, and how could it restrain their memories when they see him every day?" Tsunade said as Hiruzen sighed.

"I don't know, maybe somehow the seal made them see him differently, maybe not as their son….like I said I don't know." He said as Kushina looked back at the two.

"We have to tell them." Tsunade said as Hiruzen rubbed the back of his head.

"Yeah, this is going to be a pain in the ass." Hiruzen said as they walked in.

* * *

**Thirty minutes later**

Kushina and Minato were speechless. It wasn't everyday that you learned that you had neglected your son for most of his life without even realizing you were doing it. But the most disturbing part was the fact that someone had placed as seal on them, but who would want to do that? Maybe some people from Iwa that hated Minato? That was the only logical guess he could come up with.

"Hiruzen, we are going to see our son." Kushina said as Minato nodded.

"Are you sure that's a good idea?" He said as they looked back.

"Not sure, but if he lets us explain, then we could make him understand what happened." Minato said as Tsunade sighed.

"What about your daughters? Shouldn't you make sure they are being watched first?" Hiruzen said as Tsunade stood up.

"Don't worry I'll take care of that they wanted to see their big brother fight either way, I'll bring them there, you two, I should warn you….Naruto….isn't the same as he once was." Tsunade said as she recalled what Naruto had done to make himself stronger.

"We have to try." They said as they disappeared.

"How do you think Naruto will react?" Hiruzen said as Tsunade sighed.

"I don't know…are we sure it was a good idea for them to go see him so quickly?" Tsunade said.

"I don't even know, another thing I wonder about though, is who could possibly have the power to manage to place a seal on the fourth hokage and his wife." Hiruzen said as he started to walk towards the academy.

* * *

**AT THE ACADEMY**

Naruto was currently standing in line with the others, they were apparently having this new tournament style graduation for once. It was to determine who would become the rookie of the year since the scores were too close. So they were going to spar against each other to see how everyone would fair.

What surprised Naruto was that there was this girl joining the exam, apparently she was some foreign village, he didn't know why she was here to take a genin exam in Konoha if she was from a different village, but he felt like the reason had something to do with him. The truth was it did.

They were paired into matches as the fights got underway.

The first few matches were easy due to the fact that some of the worst students were going up. Naruto himself had easily dispatched Choji and Shikamaru, One because he had greater speed and Choji couldn't keep up, and Shikamaru because he slept through it, boy was his mother pissed.

**(IM JUST GONNA SKIP MOST OF THE MATCHES SINCE I AM TOO LAZY TO WRITE THEM)**

In the end, Naruto was pitted up against the girl from the foreign village, he still did not know the reason why she was here.

"Fight between Naruto Uzumaki Namikaze and Shizuka of Nadeshiko, you are allowed to use any and all tactics to win…begin!" Iruka said as Naruto stood there as the girl got into a stance.

"I wouldn't look so relaxed if I were you boy." Shizuka said as she got a couple of kunai out.

"If you would look closely you would notice that I am not as relaxed as you think." Naruto said as he held out his hand and brought the other one back.

Meanwhile in the crowd, Naruto's parents had just shown up.

* * *

**WITH KUSHINA AND MINATO**

As soon as Minato saw the girl, and more specifically just what country she was coming from to fight Naruto, he knew that things were going to get a lot more complicated.

"Minato isn't that-" Kushina started but Minato cut her off.

"Yes it is, but look at Naruto…he looks….different." He said as they both got a good look at their son.

He was wearing all black, and more importantly he just looked too dark and serious when he was dressed like that. The last time they could remember the way they saw him before the seals were placed on them. He was the happiest brightest kid in the world, but now he showed little emotion. And the sad part was, it was partially their faults. Sure they were under the influence of a seal, but they couldn't even fight it.

"Kushina, how do you think he will do against her?" Minato asked as they didn't know what their son was trained in, hell they didn't train him! They had no idea if he was talented or not.

"Shut up and watch." Kushina said as Minato nodded.

To their surprise, Naruto was holding his own against Shizuka. Not only that, but he seemed to be beating her at times. They didn't recognize any of the forms of Taijutsu he was using.

"Yeah! Go big brother!" Mito yelled out from across the ring.

Tsunade kept her word and had brought Mito and Miu to watch their brother fight in the Genin tournament. She had to admit, this new idea of the Shinobi Corps was a good idea for measuring the strength of Genin to be.

Naruto was currently fending off all of the girls Kunai strikes while she was getting more frustrated from the trench coat wearing boy. If anything Naruto looked like Neo when he first discovered that he was the one, fending off Agent smith with one hand.

And sure enough, after that Naruto grabbed hold of her wrist and kicked her away. She was really starting to get pissed that she was being beaten so easily. Even though her mother taught her to remain calm, she just couldn't help but get frustrated.

"THAT'S IT!" She said as as she thre multiple Kunai knives in the air and started to perform hand seals.

"SECOND STEP!" She said as she started to spin around and a volley of Kunai knives were being thrown at Naruto.

"_No! There is no possible way he can dodge all those at that age!" _Minato and Kushina thought in sync as they just looked at their son.

Naruto had the same look on his face as he always did. He just looked at the knives and he said one word.

"No." He said as he raised his hand.

And to everyone's shock and surprise, the kunai just stopped right in front of him. They just….stopped. But how? That shouldn't be possible, they couldn't detect any chakra use, if he was using any, he was using a minimum amount.

"W-What?" Shizuka said as her mother and the man who was with them were staring at Naruto with their mouths open.

"….." He didn't say a word as the Kunai fell to the ground.

Tsunade was just looking at Naruto with a calm face as his sisters looked in awe, Tsunade grinned a little as she rubbed the back of her head, where she felt one of the plugs for the matrix.

"_Good to see those skills he learned has helped him out a lot…it's almost as if he became telekinetic because of the matrix." _She thought as Naruto then ended the match with a spinning back kick.

"Its over." He said as he walked out of the ring.

"Winner Naruto Uzumaki Namikaze." Iruka said as Shizuka went to her mother.

"_Oh man, Naruto is not going to like it when he finds out WHY Shizuka was here to take the Genin exams." _Minato thought as Naruto was heading straight for them.

"Naruto that was am-" Kushina started but Naruto walked right past them.

She was shocked at first, but then she remembered what Tsunade had told them, they had been neglecting him for years. Even though it wasn't their fault, he still wasn't going to be happy to see them.

"We should have known this was going to happen." Minato said as Kushina looked down.

"What do we do?" She asked as Minato looked at her.

"First we got to explain what happened to us….and then, we do whatever it takes to get him to forgive us…whatever it takes." Minato said as Shizuka was talking to her mother.

"Do you understand now Shizuka?" Shizuka's mother said as Shizuka nodded.

"Yes, since the boy defeated me in a battle…I am now supposed to marry him." She said as her mother nodded.

"That's right, but we will wait til your older, until then, we should continue your training, surely Minato will tell his son what is going on." Her mother said as they left.

The next time they would meet, would be at the Chunin exams.


	5. Explanation

**Alright, here is the new chapter, after this, i will be going offline for a while due to some things that have come up, and the reason why it might take me so long to update lately. Is because once again my computer crashed on me, i think its time for me to stop fixing it and actually try and find a new one.**

**As of right now, i am on a friends computer typeing this up. So I'm just telling you that since there will be times when I won't update for a while. But i will try and update and write as often as i can.**

**Anyway, not sure how this chapter turned out. But hope you enjoy it.**

* * *

**Tsunade's POV**

I noticed how Naruto had left for the matrix as soon as he got out of the academy. All in all, he looked bored or unsatisfied with his victory. It was if he thought that the victory wasn't good enough. And that he always had room for improvement. I swear that kid would train himself into the ground until he dropped dead. Either way, I had left for the Namikaze Household since it was clear that Naruto would not want anyone to interrupt him while training. And we still had an agreement that nobody else besides me, Naruto, and Sarutobi were allowed to know about the matrix.

Well, either way, when Naruto gets home, I'm not sure how he will react to the story about what happened to Minato and Kushina. After all, for a while he just thought that they didn't love him and that he wasn't worth their time. All in all, this was going to be really hard to explain to him.

* * *

**AT THE NAMIKAZE COMPOUND**

"How did he do that Tsunade?" Minato said wondering how Naruto could just will those kunai to stop, especially since at the speed they were going, they would have been impossible for an academy student to stop or dodge them.

"I wish I knew, I may have taught him a few things, but all in all, he is pretty much going away for his training." Tsunade lied to Minato since the truth behind it would be considered farfetched.

"More importantly, what about that Taijutsu he was using, I didn't recognize any of the forms, and I checked with all the clans, and it is not their style of taijutsu." Kushina said while gripping her katana, how had her son become so strong?

"It's his design." Tsunade said as they looked shocked.

"Naruto created that style? When he was still in the academy?" Minato and Kushina said as they couldn't believe that an academy student could do that.

"_Not exactly, but it is a lot easier than saying that their son is being plugged into a supercomputer and downloading the information in his brain, and not to mention training in it constantly."_ Tsunade thought as she was still avoiding the truth.

"Speaking of which, where did he go?" Minato said as Naruto still had not come home.

"He probably went out to train." Sarutobi said as he walked through the door.

"But its getting late, he couldn't be out training this late." Minato said as Tsunade got a little irritated.

"And how do you know that? You haven't exactly noticed how he acts for the last couple years!" She said a little harshly while they both looked down.

"I'm sorry, but its true." She said as even though she knew it wasn't their fault, they still acted like they knew what Naruto would do.

"Big Brother is home!" Miu yelled out as everyone looked towards the door.

And of course, there was Naruto, still in his trench coat, but minus the sunglasses. But they noticed something else, when they first saw him; it was as if he was hovering off the ground. But Minato and Kushina just thought that it was their imagination. Pretty soon, Mito and Miu hugged his legs as he walked in.

"Hey little sisters." He said as he patted both of their heads.

"Where have you been? Mom and Dad have been waiting for you!" Mito said as Naruto looked shocked for a second but then went back to his calm face.

"Have they now? Well, I was a little busy and lost track of the time." He said as his sisters went over to the table.

"Mito, Miu, why don't you two go upstairs, we all have something to say to Naruto." Minato said as Naruto got even more confused.

His sisters groaned and not being able to stay so that they could hear the conversation, but they followed their father's orders either way.

"So Naruto that was a…impressive performance at the academy." Minato said as Naruto's face didn't change.

"Impressive, not really, there were areas that I needed to improve in." He said as Sarutobi just sweat dropped.

"_Damn, he really does not know how to take a compliment does he?" _Sarutobi thought as Minato sighed.

"Either way, I was actually wondering why you two were there…..I mean didn't you have important duties to do as Hokage? And not spending time at the academy watching an exam?" Naruto asked as Minato just looked at him.

"We just wanted to see our son fight, that's all." Kushina said as Naruto got even more confused.

"Okay seriously, what the hell are you two trying to pull?" Naruto said as their eyes widened.

"What are you talking about, we are congrat-" Minato started but Naruto cut him off.

"I can see that, but what I mean is just what has gotten into you two, you guys hear about some exam and you see me fight, and all of a sudden you decide I'm worth your time?" Naruto said in a cold tone as his parents were shocked at his choice of words.

"No its not like that at all…it's just….it's kind of complicated." Kushina said as Naruto looked around.

"Well, I got nowhere to go, try and explain what caused a change of heart." Naruto said as he crossed his arms and put a serious look on his face.

"You want to take a seat?" Kushina said as Naruto shook his head.

"No, I'm good right here." Naruto said as he was waiting for an explanation.

"Well, uhm, How do we explain this?" Minato asked as Naruto was getting irritated.

"If you don't want to tell me than I will just leave." He said as he started to walk away.

"We were SEALED!" Kushina said as Naruto looked back at them.

"Come again?" He said as he turned around.

Kushina sighed in relief that he actually turned around instead of walking out the door and going god knows where. The only problem now would be explaining the rest of their situation to him. And that was not going to be an easy task.

"This morning, we were going through the academy reports, and we saw your name on the list for the Genin Tournament….but…we didn't remember signing you up for the academy, or even if you were old enough." Minato said as Naruto looked at him, you couldn't see his eyes under his dark sunglasses.

"That's because you didn't, I signed myself up for the academy, since you two weren't there that day." He said as they felt even more guilty.

"Look, and when we started to think of you, we felt this burning sensation, it was painful…and we were laying on the ground, when Tsunade found us, and her and Hiruzen removed the seals, and then….the only thing we could think about was you." Kushina said as Minato nodded.

Naruto's face had not changed, it was like he was not surprised at all. But if one looked closely, you could see his eyes were full of emotion and that his hands were twitching nervously. But he quickly controlled those twitches and put his hands in his pockets.

"The seals were some sort of memory seal, or at least that is what we believe, Hiruzen wasn't an expert on seals and we never got the chance to look at the seals…so we don't know what was applied, or when." Minato said as he looked down at that.

Naruto looked at them, wondering if they were telling the truth, call him paranoid, but when the two people who have been ignoring you for most of your life suddenly turn up and say that they were sealed and that it wasn't their fault, he couldn't be sure if they were just playing a sick joke, or if they actually cared about him.

This whole situation was confusing to him, and he did not know how to react to any of it. In fact, as of right now, he was trying to think of what he was going to say to them next. After all, its not everyday your so called parents tell you that they ACTUALLY DO care for you and don't think of you as a stray pet.

"I see…." He said as he turned around.

"Wait where are you going?" Kushina asked in a panic.

"I'm going out to train, I need to think about this." Naruto said as he opened the door.

"Wait! Please stay here for a while!" Minato pleaded as Naruto didn't look back.

"Please! We're sorry, we didn't want to neglect you all those years….can you….forgive us?" Kushina said as Naruto sighed and looked at them.

"I do forgive you." He said as his parents looked up at him with hope in their eyes.

"But that doesn't mean that I trust you." He said as he walked out the door.

Those words drove a knife through his parent's hearts, what were you supposed to do when you find out that your own child didn't trust you? The answer was something that they did not have.

"When will you be back?" Kushina said with slight tears in her eyes.

"Some time." He said as they saw him walk out the door.

At this point, Kushina started to cry, even though Naruto had forgiven them, he obviously did not trust them, especially since he didn't even tell them where he was going or when he would be back. He didn't trust them with his location? That just did not settle right with his parents. Minato was currently trying to comfort Kushina as she was crying into his shoulder. Tsunade felt a little sorry for the parents, but at the same time, she was glad that Naruto wasn't going to forgive them any time soon. She was a little conflicted, but she went outside and started to walk to the bar. God knows that she needed a drink now more than ever.

As for Sarutobi, he seemed to have no reaction. To be honest, he was expecting that this was going to happen. So it wasn't really a shock to him. But at the same time, he felt sorry for both the parents and Naruto. He felt sorry for Naruto because this was probably a lot for him to take in. And he felt sorry for Kushina and Minato because their own son didn't trust them or want to be around them at the time.

"I'll leave you two alone." He said as he walked upstairs to see if Mito and Miu were asleep.

"_Well, that went better than I expected, I half expected Naruto to tear down a wall, but now, who knows what kind of training he is going through with Neo." _Sarutobi thought as he resisted the urge to light his pipe.

* * *

**Naruto's POV**

Naruto was currently jacked into the matrix, and relieving some stress by sparring with Neo. He just couldn't believe what had just happened only moments ago. His parents came out and said that they were being controlled by a seal this entire time? Seriously? A seal! A field that they were both experts in! And someone had placed a seal on them without them noticing!

He could have sworn that seal masters were trained to detect any and all seals that had been placed on anyone. But if that was the case, wouldn't they have both noticed that the other person had a seal placed on them. But if what they said was true, then maybe that burning feeling that they were felling erased their memories of even sensing the seal. GAH! This was all so confusing!

"_You seem to be angry."_Neo said as he threw Naruto into a virtual wall.

"I don't know what to think Neo…..I mean I can't trust my parents so easily, but I know I can't hate them for what happened, and god I do want to hate them, but I know that would do no good." He said as they stopped sparring for a second.

"_It would be foolish to hate them for something that they couldn't control, the same could be said about you holding the nine tailed fox in your body, there are people who hate you in the village for being its container, so in other words, if you were to hate them because of a seal that was placed on them, it would be a foolish thing to do since you in reality are in the same boat."_ Neo said as Naruto nodded.

"I know, but like I said this is hard to accept." He said as Neo nodded.

"_Why don't we get back to sparring and you can think of ways to try and improve the situation later." _Neo said as Naruto once again nodded and got back into a Muay Thai stance.

"_Good, now lets see how much you have improved."_He said as they both charged in for an attack.


	6. A Prank And Old Photos

**Okay, sorry that I haven't updated this in a while, I was trying to focus on others, and apparently I am having writers block with almost everyone of my stories. Add that on to all the new ideas i want to try out. Gah! Its frustrating! I know i shouldn't start a new story since i already got these to worry about. So maybe I will just add them on to my challenge lists. Yeah that would probably work out better.**

**Anyway, without any further waiting, here is the next chapter of Naruto The One**

* * *

**Naruto's POV**

Naruto had just finished training with Neo, it would appear that the stress and confusion that he was feeling before had completely faded away. Which was good since it would only get in the way of his training from there on out. He didn't want to have any distractions that would hinder him in the future. This was one of the reasons why he didn't socialize with that many people, because he didn't want to form any bonds that could only prove to be either distracting or could possibly hurt him in the end.

After all, it happened once when his parents got sealed, who is to say that it won't happen again? Sure with his parents it was a certain situation, but who is to say that as soon as he forms a friendship with someone, that they won't turn their backs on him when something better comes along? Naruto was not a very trusting person, as he had proven time and time again, if you wanted his trust you would have to earn it. And the only people who had done that were all of the older generation, which included the people he trained with, and of course Kiba and the owners of the Ichiraku ramen bar. No matter how serious he may be, he still liked the taste of ramen.

As of right now, he was heading home, he was flying over Konoha as he looked down below. Everything always seemed so calm from up here, you wouldn't think that their actually were criminals down there. Oh yes, even though Konoha was one of the most peaceful villages in the shinobi nations, it still had its fair share of criminals. One such example would be how Naruto had recently stopped a number of rapes from happening. They had been easy to take care of due to the fact that all of the would be rapists were common street brawlers. So they were no match for him and his enhanced reflexes.

"What to do?" He said as he suddenly saw something out of the corner of his eye.

He saw what appeared to be Anko and Itachi in an alleyway. Now even though he was mature for his age, he still had a problem with controlling his curiosity. Which is why it got the best of him most of the time. So he landed on a roof near them as he looked down at them. And what he saw next surprised him but made him smile at the same time.

Anko and Itachi were making out in the alleyway! I mean they looked like a pair of lions mating with the way they were grabbing and clawing at each other as their lips were locked. Naruto had to admit, he was a little frightened by their animalistic behavior. Hell, he expected something like that to happen when Hana and Tsume were around potential mates. But this was something else entirely.

"_Okay, time for a prank." _He said as a squid bot appeared and a microphone and voice changer appeared out of the back of it.

Imagine Anko and Itachi's surprise when they heard a man with an Australian accent start to speak as if they were in a documentary.

"_And here we see the wild Anko and Itachi engage in a vicious mating cycle, as you can see they can get very aggressive when they mate which is shown by the clawing motions at his back and the fact that it also looks as if they are trying to eat each others faces." _Naruto said through the voice changer as they looked up and saw him.

"Naruto! What the hell?!" Anko yelled out at him as the squidbot flew away. Obviously Naruto couldn't have them see the advanced technology that was in his possession. That would create all sorts of problems.

"Sorry, the moment was too perfect to pass up." Naruto said as he gave a light smile.

"Dude that is not cool!" Itachi said as Naruto saw him pout a little.

Wow, the great Itachi Uchiha pouting? Naruto did not think it was possible to happen. But it would appear that he had been proven wrong. Either way, he was laughing his ass off on the inside, and Anko and Itachi were both embarrassed and angry at the same time.

"You know one of these days, your gonna find a girl, and we are going to get you back for this!" Anko said as Naruto laughed.

"I'll believe it when I see it!" He said as he flew off.

"….Did he Just…Fly?" Anko said as they still did not know that Naruto could fly.

"I…I think he did….but how? I didn't sense any chakra?" Itachi said as he rubbed his eyes.

"Oh well Screw it…where were we?" She said as she pulled him back into a kiss.

* * *

**WITH NARUTO**

Naruto had arrived home very late, so late that most normal people would have been asleep by now. However it would appear that his parents were not normal people. They had stayed up waiting for him to come home. Apparently they actually did care for him more than most people would think. He knew it wasn't their faults that they neglected him for half of his life. But they just couldn't go back to the way things were, after all, all the hurt and pain that Naruto felt everytime they passed him off as a servant. It really hurt, it was emotionally scarring. In fact, it was one of the reasons he seemed to have a cold personality at times. Because when you go through that kind of trauma, and especially when you add in the mix of an ancient city of machines and an old war hero, you tend to change.

At times, it did bother Naruto. That he couldn't go back to the way things were. But also, he didn't really care, he had been better than he had ever been. But was it worth it? Was it worth losing the love of two of the most important people in your life? He still didn't know the answer to that question.

As he hovered past them, he noticed how Kushina had fresh tear marks rolling down her face in her sleep. And she also seemed to be clutching something in her hands. Naruto and his insatiable curiosity got the best of him as he used a calming jutsu on her so she wouldn't wake up when he took the book that was in her hands.

As he took it out of her hands, he opened it up and discovered that it wasn't actually a book, but instead it was a photo album. Of all the photos they had taken back when he was still a kid. He couldn't believe they actually still had these things, he would have thought they would have been thrown out after they both were sealed in their minds.

He looked through the first page, he noticed how they all seemed to be his baby photos. His parents had dressed him in a orange fuzzy fox outfit. He raised an eyebrow at that photo.

"They dressed me up as a fox, a fox was what destroyed a large portion of Konoha and killed many people until it was sealed in me…yet they dress me up as one? I don't understand." He said as he flipped to the next page.

"Holy shit….I haven't seen this photo in years." Naruto said as he slid a photo out of its sleeve.

It was a photo of the time when He and his mom pranked the Hyuuga compound; they had replaced their underwear with fur jockstraps, their robes with Fuzzy red robes that Hugh Heffner wouldn't wear. And his favorite part was dying their hair when they were asleep. Now that he thought about it, he only had one question.

"How the hell did we sneak in there?" He asked as he couldn't remember the reason how. And he also couldn't remember why they were doing it in the first place.

All he remembered was that someone told him that they needed to lighten up. Either that or he was watching too many old films with Neo that were messing with his mind. He ignored those thoughts as he turned to the next page. And it was around the time period where the twins were born. He was holding both of them in one arm, he smiled at the memory. He remembered that day very well, It was the first time he ever held his baby sisters. And at that moment he felt really protective of them, hell one time when he had gotten back from training in the matrix, he beat up an old drunk who was looking at them the wrong way.

But as Naruto was looking through these, he wanted to know one thing. Why were they still here? Surely if his parents were sealed, and the memories of him were distorted, then wouldn't they have gotten rid of the photo albums to prevent any memory problems? It was confusing, well at least it was until he heard a voice.

"_Even though they couldn't understand their actions, it was clear they still wanted to keep a piece of you close even when they couldn't act like parents." _Neo's voice said as Naruto turned around and saw a squid bot with Neo's voice coming out of it.

"How would you know?" Naruto asked as he examined the plugs on his arm, even after all these years he still marveled at the technology.

"_It's only a theory, not only seals are perfect, its just like how not all computer programs are perfect, some can change and others can destroy themselves." _Neo said as Naruto looked at him.

"But this isn't a computer program or a seal Neo, its two humans…my parents, it's a little different." Naruto said as he was surprised that he called them his parents.

"_I'm just offering my own words of wisdom here Kid." _Neo said as the squid bot flew out the window.

Naruto sighed and put the photo album away and started to walk upstairs to his room. He turned and looked back at his parents sleeping on the kitchen table. He decided to leave them there, if he woke them up now, he would just be bombarded with questions as to where he was so late at night. And considering the fact that he still had trouble trusting them , he wasn't exactly ready to risk the revealing of the location of his training ground. After all, there was no telling what could happen if the rest of Konoha found the technology of Machine city. For all he knew, some corrupt official could mess with the programming and possibly start the war between man and machines all over again.

Call Naruto Paranoid, but he believed that there was a high chance of that happening if anyone else was to discover the matrix. Or that one war hawk on the council might use it to train his soldiers to their full potential. But then of course, it is not like it would do them any good, after all, Neo said he seemed to be one of the few people who could use the matrix and not be killed. Plus if anyone who was foreign to the system who Neo or Naruto didn't approve of, Well, the security system would kick in and would blow their brains to bit.

It was brutal and a pain the ass to clean up, but it was very effective. And if that is what had to happen to keep the matrix safe, then so be it. Besides, it wasn't like anyone would be able to enter the machine city without him knowing. He had installed security seals and systems to help prevent anyone from just falling into it like he did.

Either way, he went up to his room, crawled into his bed and slept like a baby. Unaware of the events that would unfold later in his life.


	7. A Breakfast Conversation

**Okay, so due to a request from one of my readers, I have decided to write another chapter of Naruto The One. Now its been a little hard writing this lately, because unfortunately I have a bad case of writers block with pretty much everything, even some of the stories on another one of my accounts. But the point is Its really starting to get to me. But I guess I made a resolution to try and work on all of my stories. So here I am trying to write. **

**So enjoy.**

* * *

**Naruto's POV**

Naruto was currently up in his room stretching out his limbs. The metal plugs in his arms looked as if they were moving as he was using his limbs. In fact if you looked closely you could see that the plugs were actually sliding in and out of his skin. It was mostly because they were coming loose. However, pretty soon they were all going to fall out. The reason why is because he wouldn't need them anymore.

After some research and some engineering. He had found a way to install a new plug in his head that would replace all the ones in his arms, legs and spine. Basically what happened was that Neo sent a jolt of energy into Naruto's body, which was causing the original plugs to lose their grip and eventually some of them started to just fall out.

CLUNK! CLUNK!

In fact another two just fell out. Naruto took a break and looked at his arm, the wounds from the plugs falling out of his arm closed up as soon as they showed up. It was good to have accelerated healing. Especially when you had to deal with something like this. He couldn't imagine how bad it would have been if they fell out without him being able to heal fast. He might be in the hospital because of blood loss.

"Two down, twenty more to go." He said as he picked up the two plugs and put them in a box under his bed.

"Seriously, these things are starting to get annoying." He said as he pushed the box back under the bed and got back to doing some Kata for his martial arts styles.

He was thinking about yesterday, he knew that he had to try and do something to try and repair the mend in his family. But he just didn't know how to, everything was just so complicated lately. He decided to try and take things slow. After all, he saw it in a movie once, shit like that usually gets worked out. He did a few more punches on a wooden dummy before he decided to get completely dressed and go downstairs.

He reached into his closet and pulled out a different trench coat, he had multiple ones so that he didn't make the mistake of having to buy a new one everytime one was destroyed. Hell, that would just become a pain in the ass. Especially since he spent enough as it was on the clothes he had now. Seriously, what kind of Ninja village doesn't have a constant supply of black clothing. Well, apparently it was Konoha, but weren't Ninja supposed to be stealthy. Half of the stuff they sold in the Ninja stores was too bright.

Hell, even though too much black would stand out in some situations, at night it would be perfect, no one was going to see a man dressed in all black. But of course, considering the fact Naruto could fly and the fact he could just drop in on any situation could also help. Naruto put his sunglasses on as he holstered his sidearm. He would really need to find a way to make a bigger and better weapon. Because in some situations, the pistol wasn't going to do much.

He stood next to his door when he once again thought about what he was doing. He sighed as he ran his fingers through his hair.

_"Come on, you can't help fix this if you don't try something." _He thought as he opened his door and walked out.

About halfway down the steps he was assaulted with a variety of smells. Obviously his Mom was cooking breakfast, he was going downstairs to say goodbye to his sisters before going off to train. That had become a bit of a routine over the years and he didn't see a reason for it to change. But when he got downstairs, he was thrown off gaurd.

"Naruto, Good Morning! Would you like some breakfast?" Kushina said in a happy tone, seems like she was trying to be cheerful even though on the inside she was a little worried.

"..." Naruto was shocked, he did not know what to say to this, he hadn't been put in a situation like this for years, and now that it was happening, he couldn't remember how to react.

_"Should I take the offer? I don't know, I know we are trying to work on the rift between us, so I shouldn't deny this chance to socialize...but how the hell do I do that? My best friend is a former human who is now living in the machine world...and everyone else I got are all adults or teenagers...but they aren't related to me...shit...I really should have gotten out more." _Naruto thought as his sisters hugged his legs.

"Of course you'll have breakfast with us? Right Big Bro?" Miu and Mito asked with stars in their eyes.

_"Damn it...now I have to accept or else I'll feel like a jackass...oh what the hell." _He thought as he smiled at them.

"Sure why not, it will be nice to have a home cooked meal for a change." Naruto said as Kushina flinched at that, that obviously did not come out right.

_"Shit, That was not the right answer, now she thinks I was insulting her...think of a save." _He said as he couldn't believe he was worried about hurting his mother's feelings.

"Usually most of the stuff I get when I'm on the way to training tastes like crap." He said as Kushina brightened up a little at that.

"Well, you kids go ahead and sit down, I'll finish up in here." She said as she got back to cooking.

He walked into the dining room to see that his father was still in the house reading a newspaper, odd, shouldn't he be off at his job by now?

"If your wondering why I'm still here...its because I wanted to spend some time with my wife and children...and because someone bombed the Hokage office with a paint bomb." Minato said as Naruto chuckled a little bit at that.

He did find some comfort at the thought that someone had the balls to prank the Hokage...besides him in his pranking days. Either way, it was funny how some things turned out. But that didn't mean that he felt comfortable sitting at the table with his...family. Even then it was strange to call them that.

"Here you go!" Kushina said as she put plates of food down for everyone to eat.

Minato put his newspaper down and got a pair of chopsticks, his example was soon followed by everyone else. And Naruto, well, lets just say that he would be lying if he said he missed these moments. Especially since he actually missed his mother's cooking. Even though he just couldn't express it at the time.

"So Naruto...uhm...excited about your genin team?" Minato asked as he and the other Shinobi teachers had selected the teams based on strength and weaknesses.

Naruto knew that he was trying to make friendly conversation, so he decided to go along with it, unless he said something that pissed him off.

"To be honest, I haven't given it much thought from a personal point of view, more from a military point of view." Naruto said as he took a bite of some eggs.

"How so?" Kushina asked as she was interested to hear how her son thought.

"Well, take this, as per tradition, the Genin teams are organized based on a certain skill set, as well as considering the rankings in the academy, for example, I would be paired with the dead last and highest franking Kunoichi of the program, however, there is a flaw in this system." Naruto said as Minato suddenly was all ears.

"What the academy teaches you is only the basics and the theory of being a Shinobi, but they don't really count all the factors that could go into a shinobi, for example, one may not be a genius in books and academics, but for all you know he could be a spur of the moment genius who can think up a plan in the heat of battle, now I know for sure that the academy would not be able to find out which man or woman would fit this description until it was too late." Naruto said as he was making a lot of sense.

"Basically, how do we know that the highest ranking ones in academics would be able to apply it all to real life situations? What they should do is have a simulation...life or death to see who can make the cut." Naruto said as Mito pointed something out.

"But wouldn't that increase the death rate in the academy?" She asked as Naruto smiled at her.

"Usually yes, but say you keep the test or simulation a secret, so that way they will think it is a real attack or battle, so you can see who would crack under the pressure, and who would survive...the ones who crack, they could either be expelled, or they will need more training, those who survive, well I say they need more training anyway." Naruto said as Minato was considering the idea.

"Another idea is to increase the amount of classes and lessons in the academy, say if you went up against a swordsman of Kiri, you would be outmatched in a strict Kenjutsu battle since we don't cover Kenjutsu until you get a sensei who might be able to teach it to you, but why not turn it into a required skill? That way it could help balance our forces, the same could go for sealing arts, stealth, infiltration and interrogation skills. Being a Ninja is hard, and we can't blind them with illusions of glory, they must learn the cold hard truth behind Shinobi." Naruto said as everyone's jaw dropped.

That explanation made so much sense, but at the same time it was a little depressing.

"Now if you excuse me, I need to go get some training done, and then off to team selections...I'll...see you all later." Naruto said as he walked out of the door.

"Hey Kushina...look...we made progress! He's talking to us...and now...he gave me a great idea!" Minato said as he stood up.

"Where are you going?" She asked as her two daughters looked at him.

"To call the Shinobi council, they need to hear this." He said as he took off in a yellow flash.

"We also have to go mom, were supposed to meet Hanabi today...bye mom!" Her two daughters said as they took off out the door and she was left alone.

"Alone...eating all this food...again...why can't we all just sit down and finish a meal like a normal family?" She said even though they really couldn't be considered a normal family.


End file.
